MNT Set up vulture and remove dead code it flagged

[mvdoc]

Summary

• Add vulture configuration in pyproject.toml (paths, min_confidence 80, ignore_names = ["kwargs", "trim"] to suppress the backend **kwargs interface pattern and the documented backward-compat trim no-op in viz.plot_patch) plus .vulture_whitelist.py for pytest fixtures that are looked up by name rather than imported.
• Pin vulture>=2.14 in the dev dependency group. Running vulture from the repo root now exits 0.
• Remove the unambiguous dead code the initial scan surfaced:
  • cmd_default in cli.py (dispatch happens via argparse subcommand, nothing called it).
  • Write-only best_conn local in core.py.
  • Unused loop variable r_iter → _ in flatten/algorithm.py.
  • Unused call import in tests/test_core.py.
  • Lambda params subj → _subj in tests/test_freesurfer.py (monkeypatch.setattr callbacks that ignore their argument).
• Remove unreferenced public helpers in the flatten/ subpackage (not in __all__, no callers anywhere):
  • SurfaceFlattener.compute_distance_error / count_flipped — wrappers duplicating _compute_distance_error_jit and count_flipped_triangles that the algorithm uses directly.
  • setup_heat_geodesic / compute_heat_distance — heat-method path never wired into the pipeline; the production code uses graph Dijkstra.
  • compute_graph_distance — single-source variant superseded by compute_kring_geodesic_distances.
  • compute_both_energies_edges — edge-list variant superseded by the k-ring vectorized energy functions.
• Trim distance.py's module docstring and section header now that the heat-method block is gone.

Test plan

• vulture (run from repo root) exits 0
• vulture autoflatten scripts --exclude "autoflatten/_version.py,autoflatten/tests/" exits 0 (no API-level dead code remaining)
• pytest passes (the removed functions had no tests; the renamed lambda params and dropped call import keep test semantics identical)
• autoflatten --help still lists all subcommands (run, project, flatten, plot-flatmap, plot-projection, render-snapshots)

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Generated by Claude Code

[gemini-code-assist]

Code Review

This pull request focuses on code cleanup and the integration of the Vulture static analysis tool. It removes various unused functions, variables, and imports across the codebase, including the removal of the heat method for distance computation and several unused utility methods. Additionally, it configures Vulture in pyproject.toml and introduces a whitelist for pytest fixtures. Feedback suggests that the scripts directory included in the Vulture configuration may not exist, potentially causing the tool to fail.

[gemini-code-assist]

The scripts directory is included in the vulture configuration but does not appear to exist in the repository. This may cause vulture to fail.

[mvdoc]

scripts/ does exist — it contains 4 Python files (demo_flatten_animation.py, make_fsaverage_cut_template.py, make_subject_cut_template.py, plot_all_flatmaps.py). Including it in the vulture paths is intentional: it lets vulture see that helper functions like setup_freesurfer, identify_surface_components, and save_json are referenced (only from these scripts), so they don't get flagged as dead. vulture runs to completion with exit code 0 against the current config.

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Generated by Claude Code