From 5b8de978238364f1f25b93511c8b933ee362f321 Mon Sep 17 00:00:00 2001
From: Ludovic Henry <git@ludovic.dev>
Date: Mon, 7 Sep 2026 16:33:49 +0200
Subject: [PATCH] pyrodigal: add build-pyrodigal.yml for riscv64 wheels

Cython bindings around the Prodigal gene-prediction C library
(vendored as a git submodule); builds cleanly on riscv64 since the
CMake build falls back to its generic/swar64 scalar implementation
when no x86/ARM SIMD path is detected.
---
 .github/workflows/build-pyrodigal.yml | 80 +++++++++++++++++++++++++++
 1 file changed, 80 insertions(+)
 create mode 100644 .github/workflows/build-pyrodigal.yml

diff --git a/.github/workflows/build-pyrodigal.yml b/.github/workflows/build-pyrodigal.yml
new file mode 100644
index 000000000..3f35f5a78
--- /dev/null
+++ b/.github/workflows/build-pyrodigal.yml
@@ -0,0 +1,80 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# Based on the `wheel-linux-aarch64`/`wheel-linux-x86_64` jobs of
+# https://github.com/althonos/pyrodigal/blob/v3.7.1/.github/workflows/package.yml
+name: Build pyrodigal wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'pyrodigal version to build (PyPI version, e.g. 3.7.1)'
+        required: true
+        default: '3.7.1'
+  pull_request:
+    paths:
+      - '.github/workflows/build-pyrodigal.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '3.7.1' }}-${{ 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 3.7.1 there.
+  PYRODIGAL_VERSION: ${{ inputs.version || '3.7.1' }}
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+  MUSLLINUX_RISCV64_IMAGE: quay.io/pypa/musllinux_1_2_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build pyrodigal ${{ inputs.version || '3.7.1' }} ${{ matrix.python }}-${{ matrix.libc }}_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+        libc: [manylinux, musllinux]
+
+    steps:
+      - name: Checkout pyrodigal v${{ env.PYRODIGAL_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: althonos/pyrodigal
+          ref: v${{ env.PYRODIGAL_VERSION }}
+          submodules: true
+          persist-credentials: false
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+        env:
+          CIBW_ARCHS: riscv64
+          CIBW_BUILD: ${{ matrix.python }}-${{ matrix.libc }}_riscv64
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          CIBW_MUSLLINUX_RISCV64_IMAGE: ${{ env.MUSLLINUX_RISCV64_IMAGE }}
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: pyrodigal-${{ env.PYRODIGAL_VERSION }}-${{ matrix.python }}-${{ matrix.libc }}_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish pyrodigal ${{ inputs.version || '3.7.1' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: pyrodigal-${{ inputs.version || '3.7.1' }}-*riscv64