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connected-components-3d: add build-connected-components-3d.yml for riscv64 wheels (#1450)
* **Package**: `connected-components-3d` * **Version**: `4.1.0` * **Source**: https://github.com/seung-lab/connected-components-3d/ * **Docs**: https://github.com/seung-lab/connected-components-3d/ Compiles a Cython/C++ extension for connected-component labeling on 2D/3D images (26/18/6-connected variants). Upstream publishes no riscv64 wheel. Mirrors [upstream's `build_wheel.yml`](https://github.com/seung-lab/connected-components-3d/blob/4.1.0/.github/workflows/build_wheel.yml). **Differs from upstream** - Nothing beyond the riscv64 image. **Testing** - `fastremap` (a hard test import) has no riscv64 wheel on either index, so pip builds it from sdist. - `scipy` has no cp314t wheel anywhere, so that leg drops it and deselects the two tests that need it. **License**: OK Built on cp312; ran locally off the checkout to confirm the extension compiles and imports cleanly before pushing.
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‎.github/workflows/build-connected-components-3d.yml‎

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# SPDX-FileCopyrightText: 2026 The RISE Project
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# SPDX-License-Identifier: MIT
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---
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# Based on: https://github.com/seung-lab/connected-components-3d/blob/4.1.0/.github/workflows/build_wheel.yml
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name: Build connected-components-3d wheels (riscv64)
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on:
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workflow_dispatch:
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inputs:
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version:
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description: 'connected-components-3d version to build (git tag, e.g. 4.1.0)'
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required: true
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default: '4.1.0'
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pull_request:
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paths:
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- '.github/workflows/build-connected-components-3d.yml'
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concurrency:
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group: ${{ github.workflow }}-${{ inputs.version || '4.1.0' }}-${{ github.head_ref || github.run_id }}
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cancel-in-progress: true
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permissions:
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contents: read # to fetch code (actions/checkout)
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env:
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CC3D_VERSION: ${{ inputs.version || '4.1.0' }}
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MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
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jobs:
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setup:
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uses: $/.github/workflows/_setup.yml
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build_wheels:
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needs: [setup]
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name: Build connected-components-3d ${{ inputs.version || '4.1.0' }} ${{ matrix.python }}-manylinux_riscv64
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runs-on: ubuntu-24.04-riscv
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timeout-minutes: 60
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strategy:
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fail-fast: false
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matrix:
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include:
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- python: cp312
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scipy: scipy
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k: not test_connected_components_stack
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- python: cp313
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scipy: scipy
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k: not test_connected_components_stack
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- python: cp314
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scipy: scipy
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k: not test_connected_components_stack
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- python: cp314t
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scipy: ''
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k: not test_connected_components_stack and not test_compare_scipy
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steps:
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- name: Checkout connected-components-3d ${{ env.CC3D_VERSION }}
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uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
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with:
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repository: seung-lab/connected-components-3d
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ref: ${{ env.CC3D_VERSION }}
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persist-credentials: false
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- uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074 # v4.2.0
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with:
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output-dir: wheelhouse/
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only: ${{ matrix.python }}-manylinux_riscv64
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env:
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CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
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# numpy is a build-time requirement (headers, via pyproject.toml's
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# build-system.requires) and, despite not being declared as a
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# runtime dependency by name in pyproject.toml, an implicit one too
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# (the compiled extension calls numpy's C API at import time; it is
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# declared in install_requires in setup.py). Only our registry has
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# it for riscv64; only-binary keeps a newer PyPI release from
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# winning the resolution and then compiling from sdist.
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CIBW_ENVIRONMENT: >-
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PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
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PIP_ONLY_BINARY=numpy
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# fastremap has no riscv64 wheel on either index, so pip builds it
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# from sdist; scipy has no cp314t wheel on any index/platform yet,
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# so it and its tests are dropped on that leg only (gotcha 149).
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CIBW_TEST_REQUIRES: pytest numpy fastremap ${{ matrix.scipy }}
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# automated_test.py sits next to the unbuilt cc3d/ source package;
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# staging only the test file keeps that directory out of test_cwd
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# so `import cc3d` resolves to the installed wheel (gotcha 25).
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CIBW_TEST_SOURCES: automated_test.py
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# crackle-codec (the optional "stack" extra's codec) has no riscv64
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# wheel anywhere, so test_connected_components_stack is deselected
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# on every leg rather than building its pybind11/google_crc32c
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# dependency chain from source for one optional extra.
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CIBW_TEST_COMMAND: >-
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python -m pytest -v automated_test.py -k "${{ matrix.k }}"
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- name: Check wheel contents
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run: |
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python3 - wheelhouse/*.whl <<'EOF'
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import sys, zipfile
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names = zipfile.ZipFile(sys.argv[1]).namelist()
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exts = {n.split("/")[-1].split(".")[0] for n in names if n.endswith(".so")}
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assert exts == {"fastcc3d"}, exts
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licences = {n.rsplit("/", 1)[-1] for n in names if ".dist-info/licenses/" in n} - {""}
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assert licences == {"AUTHORS", "COPYING", "COPYING.LESSER"}, licences
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EOF
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- name: Store wheels
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uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
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with:
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name: connected-components-3d-${{ env.CC3D_VERSION }}-${{ matrix.python }}-manylinux_riscv64
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path: ./wheelhouse/*.whl
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if-no-files-found: error
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publish:
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name: Publish connected-components-3d ${{ inputs.version || '4.1.0' }}
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needs: [setup, build_wheels]
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permissions:
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contents: write
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pull-requests: write
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uses: $/.github/workflows/_publish-wheel.yml
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with:
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artifact-pattern: connected-components-3d-${{ inputs.version || '4.1.0' }}-*-manylinux_riscv64

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