mmcif: add build-mmcif.yml for riscv64 wheels

.github/workflows/build-mmcif.yml

@@ -0,0 +1,105 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on upstream's own cibuildwheel config:
+#   https://github.com/rcsb/py-mmcif/blob/5e030c223d93e0311a9133672d1c35992b271281/pyproject.toml
+name: Build mmcif wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'mmcif version to build (e.g. 1.1.1)'
+        required: true
+        default: '1.1.1'
+  pull_request:
+    paths:
+      - '.github/workflows/build-mmcif.yml'
+      - 'patches/mmcif/**'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '1.1.1' }}-${{ github.head_ref || github.run_id }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read  # to fetch code (actions/checkout)
+
+env:
+  # `inputs.version` is empty on pull_request events; default to 1.1.1 there.
+  MMCIF_VERSION: ${{ inputs.version || '1.1.1' }}
+  # Upstream cuts PyPI releases without pushing a git tag; this is the merge
+  # commit whose tree is byte-identical to the 1.1.1 sdist (mmcif/__init__.py's
+  # __version__ matches, 18 minutes before the sdist upload). Update alongside
+  # MMCIF_VERSION.
+  MMCIF_REF: 5e030c223d93e0311a9133672d1c35992b271281
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build mmcif ${{ inputs.version || '1.1.1' }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 60
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+
+    steps:
+      - name: Checkout py-mmcif ${{ env.MMCIF_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: rcsb/py-mmcif
+          ref: ${{ env.MMCIF_REF }}
+          # The C++ core (parser, tables, regex) and pybind11 are git submodules;
+          # the released sdist bundles them (README's own clone instructions use
+          # --recurse-submodules).
+          submodules: recursive
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Patch mmcif source
+        run: git apply python-wheels/patches/mmcif/${{ env.MMCIF_VERSION }}/*.patch
+
+      - name: Build and test wheel
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+
+      - name: Check the extension made it into the wheel
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          for whl in sys.argv[1:]:
+              names = zipfile.ZipFile(whl).namelist()
+              assert any(n.startswith("mmcif/core/mmciflib") and n.endswith(".so") for n in names), names
+              assert any(n.endswith(".dist-info/licenses/LICENSE") for n in names), names
+              print(whl, "ok")
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: mmcif-${{ env.MMCIF_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish mmcif ${{ inputs.version || '1.1.1' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: mmcif-${{ inputs.version || '1.1.1' }}-*-manylinux_riscv64

patches/mmcif/1.1.1/0001-build-compile-the-C-core-with-fPIC.patch

@@ -0,0 +1,39 @@
+From c4810cb4b5b938fd8c2f0bff467f1fbbd4d012ec Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Thu, 10 Sep 2026 08:07:11 +0200
+Subject: [PATCH] build: compile the C++ core with -fPIC
+
+Upstream-Status: To upstream [not submitted; this port's automation may not open issues or PRs on repos other than riseproject-dev/python-wheels]
+
+CMAKE_C_FLAGS carries -fPIC but CMAKE_CXX_FLAGS does not, so the C++
+object files that make up mmciflib-all (linked into the pybind11
+shared module mmciflib.*.so) are compiled position-dependent. This
+goes unnoticed on x86_64/aarch64, but riscv64's binutils ld enforces
+PIC strictly for shared-object relocations and segfaults while
+generating the -flto link (an assertion failure in elfnn-riscv.c),
+after first reporting the underlying cause:
+
+    relocation R_RISCV_HI20 against `a local symbol' can not be used
+    when making a shared object; recompile with -fPIC
+
+Add -fPIC to CMAKE_CXX_FLAGS to match CMAKE_C_FLAGS.
+---
+ CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 35eeaca..6571ac5 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -60,7 +60,7 @@ if (NOT CONFIGURED_ONCE)
+     #set(CMAKE_CXX_FLAGS "${warnings} ${mydefines}  -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++14  -flto "
+     #    CACHE STRING "Flags used by the compiler during all build types." FORCE)
+     #
+-    set(CMAKE_CXX_FLAGS "${warnings} ${mydefines}  -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11  -flto "
++    set(CMAKE_CXX_FLAGS "${warnings} ${mydefines}  -fno-common -fvisibility=hidden -fvisibility-inlines-hidden -std=c++11  -flto -fPIC "
+         CACHE STRING "Flags used by the compiler during all build types." FORCE)
+     #
+     set(CMAKE_C_FLAGS   "${warnings} ${mydefines}  -fPIC"
+-- 
+2.50.1 (Apple Git-155)
+