fill-voids: add build-fill-voids.yml for riscv64 wheels - #1472
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Cython/C++ extension by the seung-lab family (connected-components-3d, fastremap), no riscv64 wheel on PyPI or pypi.riseproject.dev. Mirrors upstream's own cibuildwheel job, narrowed to manylinux_riscv64, with numpy pinned to our registry for build+runtime (only-binary keeps pip from compiling it from sdist) and fastremap (a hard runtime import) built from sdist since it has no riscv64 wheel anywhere yet. automated_test.py loads its EM segmentation fixture via crackle-codec at module scope; that package has no riscv64 wheel and depends on pybind11/google_crc32c which don't either, so a patch swaps the fixture for an equivalent synthetic labeled volume built from numpy/scipy, keeping every test function and assertion unchanged.
luhenry
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…lume The hollow-sphere shells in the first synthetic test volume relied on a distance-threshold rasterization; at pixel resolution a thin circular/ spherical ring can have diagonal-only pinch points where scipy's default 4/6-connected flood fill and fill_voids' flood fill disagree on whether a cavity is enclosed (CI: test_scipy_comparison2d failed this way on cp312). Replace them with a 3x3x3 grid of non-overlapping hollow cubes with a 3-voxel-thick wall - axis-aligned rectangular walls have no diagonal ambiguity at any orientation, matching the pattern upstream's own test_2d_3d_differ already uses for its deterministic assertions.
test_scipy_comparison2d (and 3d) call fill_voids.fill(binimg, in_place=True) then run scipy's binary_fill_holes on that same binimg, which the in-place call has already mutated by that point; both functions snapshot the pristine input as orig_binimg first but never use it. Confirmed by reproducing in a plain aarch64 container (not riscv64-specific): 351 label/slice combinations checked exhaustively, comparing against the mutated binimg fails nondeterministically depending on which one runs, comparing against orig_binimg never does. Use orig_binimg in both functions; verified 5 full pytest runs green after the change.
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fill-voids2.1.2Compiles a Cython/C++ extension that fills voids in binary images. Upstream publishes no riscv64 wheel.
Mirrors upstream's
build_wheel.yml, narrowed to Linux/manylinux_riscv64.Differs from upstream
Testing
fastremapadded to test deps - hard runtime import, built from sdist (no riscv64 wheel yet).automated_test.pypatched - its fixture loads via crackle-codec, unavailable on riscv64.License: OK
Patches
0001-Fix-mutated-array-comparison-and-drop-crackle-codec.patch- To upstream (blocked). Swaps the crackle-loaded fixture for an equivalent synthetic labeled volume; also fixes a real bug where the 2D/3D scipy comparison ran against abinimgalready mutated by an earlier in-place fill call instead of the unusedorig_binimgsnapshot, reproduced independent of riscv64 (plain aarch64 container, 351 cases).Built on cp312/cp313/cp314/cp314t; CI running.