build-mdtraj.yml

# SPDX-FileCopyrightText: 2026 The RISE Project
# SPDX-License-Identifier: MIT
---
# This workflow is based on: https://github.com/mdtraj/mdtraj/blob/1.11.1.post2/.github/workflows/build.yaml
# and the test job of: https://github.com/mdtraj/mdtraj/blob/1.11.1.post2/.github/workflows/main.yaml
name: Build mdtraj wheels (riscv64)

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

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: mdtraj
      version: ${{ inputs.version }}

  build_wheels:
    needs: [setup]
    if: needs.setup.outputs.versions != '[]'
    name: Build mdtraj ${{ matrix.version }} ${{ matrix.python }}-manylinux_riscv64
    runs-on: ubuntu-24.04-riscv
    timeout-minutes: 180
    strategy:
      fail-fast: false
      matrix:
        version: ${{ fromJSON(needs.setup.outputs.versions) }}
        python: ["cp312", "cp313", "cp314"]

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

    steps:
      - name: Checkout mdtraj ${{ env.MDTRAJ_VERSION }}
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
        with:
          repository: mdtraj/mdtraj
          ref: ${{ env.MDTRAJ_VERSION }}
          fetch-depth: 0  # versioneer derives the version from `git describe`
          persist-credentials: false

      - name: Checkout python-wheels
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
        with:
          path: python-wheels
          persist-credentials: false

      - name: Apply patches
        run: git apply python-wheels/patches/mdtraj/${{ env.MDTRAJ_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/
            PIP_ONLY_BINARY=numpy,scipy,pandas,tables,blosc2,numexpr,ndindex,msgpack,pydantic-core,netcdf4,cftime
          # Upstream's wheel job only smoke-tests; also run its CI suite against the wheel,
          # with its conda test env minus openmm (no riscv64 build; those tests skip).
          CIBW_TEST_EXTRAS: all
          # pyparsing 3.3.3 rewrote infix_notation as a shunting-yard parser that takes the
          # first operator in op_list order without backtracking. mdtraj sorts its operators
          # alphabetically, so '>' wins over '>=' and test_binary_selection_operator fails on
          # 'name >= 1' on every arch (x86_64 too, with upstream's PyPI wheel); 3.3.2 passes
          # (gotchas 355, 583). Upstream leaves pyparsing unpinned.
          CIBW_TEST_REQUIRES: 'gsd>=2.8 pyparsing<3.3.3'
          CIBW_TEST_SOURCES: tests pyproject.toml
          # Deselected for riscv64 rounding at a histogram bin edge (gotcha 304), not a wrong
          # result: test_compare_rdf_t_master compares to a reference file that matches the
          # x86 SSE distance kernel bit for bit. riscv64 builds the scalar vectorize_generic.h
          # kernel, and GCC contracts its float32 multiply-adds to fmadd.s, so a few pair
          # distances land across a 0.005 nm bin edge: 18/20000 elements off, as 9 adjacent-bin
          # pairs (e.g. [20,32]/[20,33]). On x86_64,
          # building with -D__NO_INTRINSICS -mfma -ffp-contract=fast gives the same 18
          # elements with the same values; without -mfma it passes; and mdtraj's own numpy
          # path (opt=False) misses this reference file at 10 elements.
          CIBW_TEST_COMMAND: >-
            python -c "import mdtraj; print(mdtraj.__version__)" &&
            mdconvert -h &&
            mdinspect -h &&
            pytest -n logical --durations=10 tests/ -r fE --color=yes
            --deselect tests/test_rdf.py::test_compare_rdf_t_master

      - name: Check the wheel ships the licences and the compiled extensions
        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") and ".libs/" not in n}
          assert exts == {"xtc", "trr", "dcd", "dtr", "_rmsd", "_lprmsd", "_geometry", "drid", "neighbors", "neighborlist"}, exts
          assert "mdtraj/core/lib/libtheobald.a" in names, names
          licences = {n.rsplit("/", 1)[-1] for n in names if ".dist-info/licenses/" in n} - {""}
          expected = {"LICENSE", "LICENSE.dtrplugin", "LICENSE.munkres", "LICENSE.openmm", "LICENSE.vmd-plugins", "LICENSE.xdrfile"}
          assert licences == expected, licences
          # -fopenmp makes auditwheel vendor the image's libgomp, hence the gpl_sources job.
          assert any(n.startswith("mdtraj.libs/libgomp") for n in names), [n for n in names if ".libs/" in n]
          EOF

      - name: Store wheels
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
        with:
          name: mdtraj-${{ env.MDTRAJ_VERSION }}-${{ 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
    runs-on: ubuntu-24.04-riscv

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

    steps:
      - name: Checkout python-wheels
        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
        with:
          persist-credentials: false

      - 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: mdtraj-${{ env.MDTRAJ_VERSION }}-gpl-sources
          path: gpl-sources.tar
          if-no-files-found: error

  publish:
    name: Publish mdtraj ${{ 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: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
    with:
      artifact-pattern: mdtraj-${{ matrix.version }}-*-manylinux_riscv64
      gpl-sources-artifact: mdtraj-${{ matrix.version }}-gpl-sources
      gpl-sources-description: gcc