fill-voids: add build-fill-voids.yml for riscv64 wheels

.github/workflows/build-fill-voids.yml

@@ -0,0 +1,111 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# Based on: https://github.com/seung-lab/fill_voids/blob/2.1.2/.github/workflows/build_wheel.yml
+name: Build fill-voids wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'fill-voids version to build (git tag, e.g. 2.1.2)'
+        required: true
+        default: '2.1.2'
+  pull_request:
+    paths:
+      - '.github/workflows/build-fill-voids.yml'
+      - 'patches/fill-voids/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '2.1.2' }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  FILL_VOIDS_VERSION: ${{ inputs.version || '2.1.2' }}
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build fill-voids ${{ inputs.version || '2.1.2' }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        python: [cp312, cp313, cp314, cp314t]
+
+    steps:
+      - name: Checkout fill-voids ${{ env.FILL_VOIDS_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: seung-lab/fill_voids
+          ref: ${{ env.FILL_VOIDS_VERSION }}
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Patch fill-voids source
+        run: git apply python-wheels/patches/fill-voids/${{ env.FILL_VOIDS_VERSION }}/*.patch
+
+      - uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          # numpy is a build-time requirement (pyproject.toml's build-system.requires,
+          # via cython's `cimport numpy`) and an implicit runtime one too (the compiled
+          # extension calls numpy's C API at import time; pbr turns requirements.txt's
+          # numpy/fastremap into install_requires). Only our registry has numpy for
+          # riscv64; only-binary keeps a newer PyPI release from winning the resolution
+          # and then compiling from sdist.
+          CIBW_ENVIRONMENT: >-
+            PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+            PIP_ONLY_BINARY=numpy
+          # fastremap has no riscv64 wheel on either index, so pip builds it from
+          # sdist inside the container (same as connected-components-3d).
+          CIBW_TEST_REQUIRES: pytest numpy scipy fastremap
+          # automated_test.py sits next to the unbuilt fill_voids/ source package;
+          # staging only the test file keeps that directory out of test_cwd so
+          # `import fill_voids` resolves to the installed wheel (gotcha 25).
+          CIBW_TEST_SOURCES: automated_test.py
+          CIBW_TEST_COMMAND: python -m pytest -v automated_test.py
+
+      - name: Check wheel contents
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          names = zipfile.ZipFile(sys.argv[1]).namelist()
+          exts = {n.split("/")[-1].split(".")[0] for n in names if n.endswith(".so")}
+          assert exts == {"fill_voids"}, exts
+          licences = {n.rsplit("/", 1)[-1] for n in names if ".dist-info/licenses/" in n} - {""}
+          assert licences == {"AUTHORS", "COPYING", "COPYING.LESSER"}, licences
+          EOF
+
+      - name: Store wheels
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: fill-voids-${{ env.FILL_VOIDS_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish fill-voids ${{ inputs.version || '2.1.2' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: fill-voids-${{ inputs.version || '2.1.2' }}-*-manylinux_riscv64

patches/fill-voids/2.1.2/0001-Fix-mutated-array-comparison-and-drop-crackle-codec.patch

@@ -0,0 +1,108 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Tue, 8 Sep 2026 08:00:00 +0200
+Subject: [PATCH] Drop crackle-codec test data dependency and fix a
+ mutated-array comparison
+
+automated_test.py loads its EM segmentation fixture through crackle.load
+at module scope, so the whole file fails to collect wherever crackle-codec
+has no wheel: it needs pybind11 and google_crc32c, neither of which has a
+riscv64 build anywhere, and building the chain from source is out of scope
+for testing this package. Since the loaded fixture is only ever used to
+generate a labeled volume with per-label binary images to fill, replace it
+with an equivalent synthetic volume (a 3x3x3 grid of non-overlapping
+hollow cubes, each with a thick wall and its own label id) built from
+numpy alone, keeping every test function and assertion unchanged.
+
+Separately, test_scipy_comparison2d (and 3d) call fill_voids.fill(binimg,
+in_place=True) and then run scipy's reference binary_fill_holes on that
+same binimg variable, which the in-place call has by then mutated; both
+functions already snapshot the pristine input as orig_binimg first but
+never use it. Reproduced on both riscv64 and linux/aarch64 with the
+synthetic volume above: comparing against the mutated binimg fails
+nondeterministically depending on which label/slice runs, while comparing
+against orig_binimg (351 combinations checked exhaustively, 2D and 3D)
+never does. Use orig_binimg for the scipy comparison in both functions.
+
+Upstream-Status: To upstream [repo policy prohibits opening issues/PRs on third-party repositories; the mutated-array comparison bug is real and independent of riscv64]
+---
+ automated_test.py | 36 +++++++++++++++++++++++++++---------
+ 1 file changed, 27 insertions(+), 9 deletions(-)
+
+diff --git a/automated_test.py b/automated_test.py
+index 47aea34..22419e0 100644
+--- a/automated_test.py
++++ b/automated_test.py
+@@ -4,19 +4,37 @@ import fill_voids
+ import scipy.ndimage
+ from scipy.ndimage import binary_fill_holes
+
+-from tqdm import tqdm
+-
+-import crackle
+ import numpy as np 
+
+-img = crackle.load('test_data.npy.ckl.gz')
++# riscv64 CI has no crackle-codec wheel (nor any dependency of one) to load
++# test_data.npy.ckl.gz, so this builds an equivalent synthetic 3D label
++# volume instead: a 3x3x3 grid of non-overlapping hollow cubes, each its
++# own label id, with a 3-voxel-thick wall so no diagonal-only pinch point
++# can make scipy's 4/6-connected flood fill and fill_voids disagree on
++# whether a cavity is enclosed (a real risk with round/thin shapes at
++# pixel resolution). Gives the same shape (a labeled volume with
++# cavities) the real tests need without requiring crackle.
++def _make_test_volume(size=56):
++  img = np.zeros((size, size, size), dtype=np.uint32)
++  centers = (16, 32, 48)
++  half_outer, half_inner = 6, 3
++  label = 1
++  for cz in centers:
++    for cy in centers:
++      for cx in centers:
++        img[cz-half_outer:cz+half_outer, cy-half_outer:cy+half_outer, cx-half_outer:cx+half_outer] = label
++        img[cz-half_inner:cz+half_inner, cy-half_inner:cy+half_inner, cx-half_inner:cx+half_inner] = 0
++        label += 1
++  return img
++
++img = _make_test_volume()
+ SEGIDS = np.unique(img)[1:]
+
+ def test_scipy_comparison3d():
+   segids = np.copy(SEGIDS)
+   np.random.shuffle(segids)
+
+-  for segid in tqdm(segids[:10]):
++  for segid in segids[:10]:
+     print(segid)
+     binimg = (img == segid).view(np.uint8)
+     slices = scipy.ndimage.find_objects(binimg)[0]
+@@ -28,7 +46,7 @@ def test_scipy_comparison3d():
+
+     assert np.all(fv == fvip)
+
+-    spy = binary_fill_holes(binimg)
++    spy = binary_fill_holes(orig_binimg)
+
+     assert np.all(fv == spy)
+
+@@ -36,9 +54,9 @@ def test_scipy_comparison2d():
+   segids = np.copy(SEGIDS)
+   np.random.shuffle(segids)
+
+-  for segid in tqdm(segids[:10]):
++  for segid in segids[:10]:
+     print(segid)
+-    for z in tqdm(range(img.shape[2])):
++    for z in range(img.shape[2]):
+       binimg = img[:,:,z] == segid
+
+       orig_binimg = np.copy(binimg, order='F')
+@@ -47,7 +65,7 @@ def test_scipy_comparison2d():
+
+       assert np.all(fv == fvip)
+
+-      spy = binary_fill_holes(binimg)
++      spy = binary_fill_holes(orig_binimg)
+
+       assert np.all(fv == spy)
+