From bd8c5b83b8c62e79d3329de5f360aa9ddae08479 Mon Sep 17 00:00:00 2001
From: Ludovic Henry <git@ludovic.dev>
Date: Thu, 15 Oct 2026 18:58:52 +0000
Subject: [PATCH] port: add cutadapt riscv64 wheel build

cutadapt compiles four Cython extensions (_align, qualtrim, info,
_kmer_finder) for adapter trimming of sequencing reads. PyPI 5.2 ships
manylinux_x86_64/win_amd64/macOS wheels but no riscv64; its one
compiled runtime dependency, dnaio, already publishes riscv64 wheels
on this registry.

Mirrors upstream's wheels job in .github/workflows/ci.yml: plain
cibuildwheel, no Linux-specific before-build steps (pyproject.toml's
own [tool.cibuildwheel] table carries the CFLAGS/test-command and
applies unchanged). Matrix drops cp314/cp314t to match upstream's own
CIBW_SKIP: cp314*.
---
 .github/workflows/build-cutadapt.yml | 101 +++++++++++++++++++++++++++
 docs/packages/cutadapt.yaml          |   5 ++
 2 files changed, 106 insertions(+)
 create mode 100644 .github/workflows/build-cutadapt.yml
 create mode 100644 docs/packages/cutadapt.yaml

diff --git a/.github/workflows/build-cutadapt.yml b/.github/workflows/build-cutadapt.yml
new file mode 100644
index 000000000000..dd824217c2a9
--- /dev/null
+++ b/.github/workflows/build-cutadapt.yml
@@ -0,0 +1,101 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on: https://github.com/marcelm/cutadapt/blob/v5.2/.github/workflows/ci.yml
+name: Build cutadapt wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'Version glob to (re)build; empty builds every version of docs/packages/cutadapt.yaml not released yet'
+        required: false
+        default: ''
+  pull_request:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-cutadapt.yml'
+      - 'docs/packages/cutadapt.yaml'
+  push:
+    branches: [main]
+    paths:
+      - '.github/workflows/build-cutadapt.yml'
+      - 'docs/packages/cutadapt.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: cutadapt
+      version: ${{ inputs.version }}
+
+  build_wheels:
+    needs: [setup]
+    if: needs.setup.outputs.versions != '[]'
+    name: Build cutadapt ${{ 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) }}
+        # Upstream's own CIBW_SKIP is cp314*; dnaio is our only other riscv64
+        # blocker and already covers cp312/cp313 here.
+        python:
+          - "cp312"
+          - "cp313"
+
+    env:
+      CUTADAPT_VERSION: ${{ matrix.version }}
+
+    steps:
+      - name: Checkout cutadapt v${{ env.CUTADAPT_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: marcelm/cutadapt
+          ref: v${{ env.CUTADAPT_VERSION }}
+          persist-credentials: false
+
+      - uses: pypa/cibuildwheel@1828c10ab37f080699c7b81cea34097c684a7074  # v4.2.0
+        with:
+          output-dir: wheelhouse/
+          only: ${{ matrix.python }}-manylinux_riscv64
+        env:
+          CIBW_MANYLINUX_RISCV64_IMAGE: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          # Shallow checkout has no tag history for setuptools_scm to read.
+          CIBW_ENVIRONMENT: >-
+            SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CUTADAPT=${{ env.CUTADAPT_VERSION }}
+            PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: cutadapt-${{ env.CUTADAPT_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish cutadapt ${{ 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: ${{ secrets.RISEPROJECT_APP_PRIVATE_KEY }}
+    with:
+      artifact-pattern: cutadapt-${{ matrix.version }}-*-manylinux_riscv64
diff --git a/docs/packages/cutadapt.yaml b/docs/packages/cutadapt.yaml
new file mode 100644
index 000000000000..90ba4e5beaa6
--- /dev/null
+++ b/docs/packages/cutadapt.yaml
@@ -0,0 +1,5 @@
+package-name: cutadapt
+source-code: https://github.com/marcelm/cutadapt/
+license: MIT
+versions:
+- version: 5.2