python-wheels/.github/workflows/build-pybedtools.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` job of
# https://github.com/daler/pybedtools/blob/v0.12.1/.github/workflows/main.yml
name: Build pybedtools wheels (riscv64)

on:
  workflow_dispatch:
    inputs:
      version:
        description: 'Version glob to (re)build; empty builds every version of docs/packages/pybedtools.yaml not released yet'
        required: false
        default: ''
  pull_request:
    branches: [main]
    paths:
      - '.github/workflows/build-pybedtools.yml'
      - 'docs/packages/pybedtools.yaml'
  push:
    branches: [main]
    paths:
      - '.github/workflows/build-pybedtools.yml'
      - 'docs/packages/pybedtools.yaml'

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: pybedtools
      version: ${{ inputs.version }}

  build_wheels:
    needs: [setup]
    if: needs.setup.outputs.versions != '[]'
    name: Build pybedtools ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
    runs-on: ubuntu-24.04-riscv
    timeout-minutes: 60
    strategy:
      fail-fast: false
      matrix:
        version: ${{ fromJSON(needs.setup.outputs.versions) }}
        # numpy (as of 2.5.0) floors at cp312, and pandas has no cp314t wheel on
        # the registry, so the intersection of pybedtools' own cp39-cp314 matrix
        # with what numpy/pandas/pysam actually provide here is cp312-cp314.
        python: ['cp312', 'cp313', 'cp314']

    env:
      PYBEDTOOLS_VERSION: ${{ matrix.version }}

    steps:
      - name: Checkout pybedtools v${{ env.PYBEDTOOLS_VERSION }}
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
        with:
          repository: daler/pybedtools
          ref: v${{ env.PYBEDTOOLS_VERSION }}
          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_BEFORE_BUILD: "pip install 'cython>3.0' setuptools && python setup.py cythonize"
          CIBW_TEST_REQUIRES: numpy pysam
          CIBW_TEST_COMMAND: >-
            python -c "import pybedtools; from pybedtools.cbedtools import create_interval_from_list; iv = create_interval_from_list(['chr1', '1', '100']); assert str(iv).startswith('chr1'), iv; print('ok')"
          CIBW_ENVIRONMENT: PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/

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

  publish:
    name: Publish pybedtools ${{ matrix.version }}
    needs: [setup, build_wheels]
    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: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
    with:
      artifact-pattern: pybedtools-${{ matrix.version }}-*-manylinux_riscv64