scikit-bio: Add version 0.7.3

.github/workflows/build-scikit-bio.yml

@@ -0,0 +1,163 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on the `build_wheels` job of
+# https://github.com/scikit-bio/scikit-bio/blob/0.7.3/.github/workflows/wheels.yml
+name: Build scikit-bio wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version glob to (re)build; empty builds every version of docs/packages/scikit-bio.yaml not released yet'
+        required: false
+        default: ''
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-scikit-bio.yml'
+      - 'docs/packages/scikit-bio.yaml'
+      - 'patches/scikit-bio/**'
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-scikit-bio.yml'
+      - 'docs/packages/scikit-bio.yaml'
+      - 'patches/scikit-bio/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+    with:
+      package: scikit-bio
+      version: ${{ inputs.version }}
+
+  build_wheels:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    name: Build scikit-bio ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+        # Matches upstream's own CIBW_BUILD: no free-threaded wheels are published.
+        # No cp310/cp311: the h5py and biom-format runtime deps have riscv64 wheels for cp312+ only.
+        python:
+          - "cp312"
+          - "cp313"
+          - "cp314"
+
+    env:
+      SCIKIT_BIO_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout scikit-bio ${{ env.SCIKIT_BIO_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: scikit-bio/scikit-bio
+          ref: ${{ env.SCIKIT_BIO_VERSION }}
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Patch scikit-bio source
+        run: git apply python-wheels/patches/scikit-bio/${{ env.SCIKIT_BIO_VERSION }}/*.patch
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          CIBW_ENVIRONMENT: PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+          # Without this, pip resolves the runtime dep pandas>=1.5.0 to PyPI's newest
+          # release, which our registry hasn't built yet and whose sdist fails on
+          # riscv64 (xsimd has no generic/scalar load_unaligned/reduce_add/broadcast
+          # there). PIP_PREFER_BINARY makes it take our registry's older wheel-backed
+          # pandas instead (gotcha 354; test-phase only, per gotcha 12).
+          CIBW_TEST_ENVIRONMENT: PIP_PREFER_BINARY=1
+          CIBW_TEST_COMMAND: python -m skbio.test
+
+      - name: Check the C extensions made it into the wheel
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          for whl in sys.argv[1:]:
+              names = [n for n in zipfile.ZipFile(whl).namelist() if n.endswith(".so")]
+              assert len(names) == 7, (whl, names)
+              print(whl, "ok")
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: scikit-bio-${{ env.SCIKIT_BIO_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  gpl_sources:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+    name: Collect GPL sources (gcc) for scikit-bio ${{ matrix.version }}
+    runs-on: ubuntu-24.04-riscv
+
+    env:
+      SCIKIT_BIO_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          persist-credentials: false
+
+      # The extensions build with -fopenmp, so auditwheel vendors the image's libgomp.
+      - uses: ./actions/collect-gpl-sources
+        with:
+          image: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          packages: gcc
+          output: gpl-sources.tar
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: scikit-bio-${{ env.SCIKIT_BIO_VERSION }}-gpl-sources
+          path: gpl-sources.tar
+          if-no-files-found: error
+
+  publish:
+    name: Publish scikit-bio ${{ matrix.version }}
+    needs: [setup, build_wheels, gpl_sources]
+    if: needs.setup.outputs.versions != '[]'
+    strategy:
+      fail-fast: false
+      matrix:
+        version: ${{ fromJSON(needs.setup.outputs.versions) }}
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    secrets:
+      app-private-key: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
+    with:
+      artifact-pattern: scikit-bio-${{ matrix.version }}-*-manylinux_riscv64
+      gpl-sources-artifact: scikit-bio-${{ matrix.version }}-gpl-sources
+      gpl-sources-description: gcc

docs/packages/scikit-bio.yaml

@@ -0,0 +1,5 @@
+package-name: scikit-bio
+source-code: https://github.com/scikit-bio/scikit-bio
+license: BSD-3-Clause
+versions:
+- version: 0.7.3

patches/scikit-bio/0.7.3/0001-use-schedule-static-for-the-dynamic-OpenMP-loops-in-.patch

@@ -0,0 +1,55 @@
+From 7641767e67e2affd82ba59131e59e02be8435c74 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Fri, 23 Oct 2026 17:48:26 +0000
+Subject: [PATCH] use schedule(static) for the dynamic OpenMP loops in
+ _c_me.pyx
+
+Upstream-Status: Inappropriate [works around a libgomp defect on the riscv64 runners, riseproject-dev/python-wheels#617]
+
+libgomp's dynamic and guided work-share schedules fault on the riscv64
+machines these wheels are built and tested on, while schedule(static)
+is clean (see the LightGBM and healpy patches in this repository).
+
+The cp312 job segfaulted in tree/tests/test_me.py::test_bme_real, with
+the Python stack ending at skbio/tree/_me.py's _bme calling
+_bal_avgdist_nest. That function's only parallel loop is a
+prange(..., schedule="dynamic"), which compiles to
+GOMP_loop_nonmonotonic_dynamic_start/next. The cp313 and cp314 jobs ran
+the same test green, as expected of this intermittent fault.
+
+_c_me.pyx has exactly two dynamic pranges, in _bal_avgdist_nest and
+_bal_min_branch_p; every other prange in scikit-bio leaves the schedule
+unset, which GCC compiles as static. Both loops do independent work per
+chunk of clades and write disjoint outputs, so the schedule only changes
+which thread takes which chunk, not the result. Moving both to static
+leaves the extension with no calls into libgomp's dynamic or guided
+iterators. Revert once the runners' toolchain is fixed.
+---
+ skbio/tree/_c_me.pyx | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/skbio/tree/_c_me.pyx b/skbio/tree/_c_me.pyx
+index 1a7b239..4b6096b 100644
+--- a/skbio/tree/_c_me.pyx
++++ b/skbio/tree/_c_me.pyx
+@@ -1031,7 +1031,7 @@ def _bal_min_branch_p(
+
+     # Parallel phase: Do calculations within chunks of clades.
+
+-    for ichu in prange(nchu, nogil=True, schedule="dynamic"):
++    for ichu in prange(nchu, nogil=True, schedule="static"):
+         for icla in range(chunks[ichu], chunks[ichu + 1]):
+             i = clades[icla]
+             min_i = roots[i]
+@@ -2256,7 +2256,7 @@ def _bal_avgdist_nest(
+     # number of branches from insertion point to any node
+     cdef Py_ssize_t deg
+
+-    for ichu in prange(nchu, nogil=True, schedule="dynamic"):
++    for ichu in prange(nchu, nogil=True, schedule="static"):
+         iseg = chusegs[ichu]  # next segment index
+         seg = segs[iseg]
+         lvl = lvls[iseg - 1] if iseg else -1  # current segment's level
+-- 
+2.43.0
+