[demianw]

What was wrong

Part of the dead code listed in #107, restricted to tract_math:

• tract_querier/tract_math/tract_obb.py (1,281 lines): the only function used outside the module is prototype_tract (by the tract_prototype_median and tract_prototype_mean operations; git grep over the whole repository finds no other import of tract_obb or of any of its names). A transitive call graph from prototype_tract (AST walk over the module's names) reaches only Box2D, Box3D, orthogonal_vector, box_cut and all_obb_3d_along_tract. The other 22 top-level definitions (738 lines) are unreachable: Box3DRich, all_obb_2d, all_obb_3d, all_obb_3d_nr, all_obb_3d_old, point_coverage_by_level, draw_boxes_2d, draw_box_2d, draw_box_3d (pylab/mayavi plotting), oriented_trace, trace, get_most_probable_trace, get_level, overlapping_boxes, containing_boxes, min_max, overlap_vtk, obb_tree_dfs, obb_tree_dfs_recursive, obb_tree_level, obb_tree_level_dfs, obb_from_tractography. All the debug print calls of the module were in them.
• tensor_operations.tract_expand_tensor_metrics: no callers, and could not run (uses the undefined name new_scalar_data_flat).
• scripts/cli_tract_math.py:11: an unused copy of the tract_math_operation decorator. Operations are registered by tract_querier.tract_math.decorator.tract_math_operation and collected with inspect.getmembers; the copy in the script is never applied.

None of the removed functions is a decorator-registered operation.

The change

Delete the definitions above and the NumPy imports that only they used (arccos, sign, cov, inf, pi, numpy.linalg.solve); pyflakes reports no unused names in tract_obb.py afterwards. The remaining code is unchanged. tract_obb.py goes from 1,281 to 500 lines.

Testing

• The registered operations (sorted(tract_querier.tract_math.operations), 32 operations) and the full tract_math --help output are byte-identical before (master) and after.
• python -m pytest -q -p no:cacheprovider tract_querier: 42 passed, 1 skipped (pre-existing unconditional skip).
• On master tract_obb cannot be imported with NumPy 2 (numpy.in1d, fixed in BUG: Fix crashing tract_math operations #143), so the prototype operations cannot run on this branch alone. I merged this branch with BUG: Fix crashing tract_math operations #143 locally (resolving the import-line conflict as below): the BUG: Fix crashing tract_math operations #143 prototype tests pass, tract_prototype_median and tract_prototype_mean (smooth order 0 and 1) run on 100 tracts of the test data, and the whole suite passed (52 passed, 1 skipped) in 9 of 10 runs; the one failing run was not captured and did not recur, most likely the known flaky test_not_in (TST: Fix random failures of test_not_in #97).
• Docs build (make -C doc html): succeeded with the same 20 warnings as master.

Merge order

Merge after #143 and #144. It conflicts with #143 on the from numpy import (...) block of tract_obb.py (resolution: keep this PR's shorter list with isin and ptp from #143) and on the removed all_obb_3d (take this PR's deletion). #144 also edits scripts/cli_tract_math.py (removes the traceback import next to the deleted decorator); a local merge of the two is clean. Local merges with #145 and #146 are clean too. The rest of #107 (outside tract_math) is handled in a separate PR (#136).

Part of #107

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