python-wheels/.github/workflows/build-biopython.yml at main · riseproject-dev/python-wheels · GitHub

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# SPDX-FileCopyrightText: 2026 The RISE Project
# SPDX-License-Identifier: MIT
---
# This workflow is based on the `build_wheels` and `test_macos` jobs of
# https://github.com/biopython/biopython/blob/biopython-188/.github/workflows/ci.yml
name: Build biopython wheels (riscv64)

on:
  workflow_dispatch:
    inputs:
      version:
        description: 'biopython version to build (e.g. 1.88)'
        required: true
        default: '1.88'
  pull_request:
    paths:
      - '.github/workflows/build-biopython.yml'

concurrency:
  group: ${{ github.workflow }}-${{ inputs.version || '1.88' }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true

permissions:
  contents: read  # to fetch code (actions/checkout)

env:
  BIOPYTHON_VERSION: ${{ inputs.version || '1.88' }}
  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64

jobs:
  build_wheels:
    name: Build biopython ${{ inputs.version || '1.88' }} ${{ matrix.python }}-manylinux_riscv64
    runs-on: ubuntu-24.04-riscv
    timeout-minutes: 120
    strategy:
      fail-fast: false
      matrix:
        python:
          - "cp312"
          - "cp313"
          - "cp314"
          - "cp314t"

    steps:
      # Upstream tags releases as `biopython-<version without the dot>`.
      - name: Resolve upstream tag
        run: echo "BIOPYTHON_TAG=biopython-${BIOPYTHON_VERSION//./}" >> "$GITHUB_ENV"

      - name: Checkout biopython ${{ env.BIOPYTHON_VERSION }}
        uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0  # v7.0.0
        with:
          repository: biopython/biopython
          ref: ${{ env.BIOPYTHON_TAG }}
          persist-credentials: false

      - 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/
          # run_tests.py enumerates doctest modules by walking `Tests/..` and some
          # tests open data through `../Bio` and `../Doc`, so reproduce upstream's
          # checkout layout around Tests/. Nothing here shadows the wheel: every
          # command runs from Tests/, which is what lands on sys.path[0].
          CIBW_TEST_SOURCES: Tests Bio BioSQL Doc
          # Upstream's macOS/Windows test jobs install only numpy; setuptools is
          # imported by run_tests.py itself.
          CIBW_TEST_REQUIRES: numpy setuptools
          CIBW_TEST_COMMAND: >-
            cd Tests &&
            python -c "import importlib; [importlib.import_module(m) for m in ('Bio.Align._aligncore', 'Bio.Align._alignmentcounts', 'Bio.Align._codonaligner', 'Bio.Align._pairwisealigner', 'Bio.Align.substitution_matrices._arraycore', 'Bio.cpairwise2', 'Bio.Nexus.cnexus', 'Bio.motifs._pwm', 'Bio.Cluster._cluster', 'Bio.PDB.ccealign', 'Bio.PDB.kdtrees', 'Bio.PDB._bcif_helper', 'Bio.SeqIO._twoBitIO')]" &&
            python run_tests.py --offline

      - 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) == 13, (whl, names)
              print(whl, "ok")
          EOF

      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
        with:
          name: biopython-${{ env.BIOPYTHON_VERSION }}-${{ matrix.python }}-manylinux_riscv64
          path: wheelhouse/*.whl
          if-no-files-found: error

  publish:
    name: Publish biopython ${{ inputs.version || '1.88' }} to GitLab
    needs: [build_wheels]
    runs-on: ubuntu-latest
    permissions:
      contents: write
      pull-requests: write

    steps:
      - name: Publish wheels and open docs PR
        uses: riseproject-dev/python-wheels/actions/publish-wheels@main
        with:
          artifact-pattern: biopython-${{ env.BIOPYTHON_VERSION }}-*-manylinux_riscv64
          gitlab-username: ${{ vars.GITLAB_DEPLOY_USER }}
          gitlab-token: ${{ secrets.GITLAB_DEPLOY_TOKEN }}
          gitlab-project-id: ${{ vars.GITLAB_PROJECT_ID }}
          gh-token: ${{ secrets.GITHUB_TOKEN }}