pysam: add build-pysam.yml for riscv64 wheels

.github/workflows/build-pysam.yml

@@ -0,0 +1,109 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on the `build_wheels` job of
+# https://github.com/pysam-developers/pysam/blob/v0.24.1/.github/workflows/release.yaml
+name: Build pysam wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'pysam version to build (e.g. 0.24.1)'
+        required: true
+        default: '0.24.1'
+  pull_request:
+    paths:
+      - '.github/workflows/build-pysam.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '0.24.1' }}-${{ 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 0.24.1 there.
+  PYSAM_VERSION: ${{ inputs.version || '0.24.1' }}
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build pysam ${{ inputs.version || '0.24.1' }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+
+    steps:
+      - name: Checkout pysam v${{ env.PYSAM_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: pysam-developers/pysam
+          ref: v${{ env.PYSAM_VERSION }}
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Patch pysam source
+        run: git apply python-wheels/patches/pysam/${{ env.PYSAM_VERSION }}/00*.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: ${{ env.MANYLINUX_RISCV64_IMAGE }}
+          # No libcurl-devel in the build image (as build-pybigwig.yml), so htslib configures
+          # without remote-URL support; pysam's own tests self-skip on HAVE_LIBCURL for that.
+          # samtools/bcftools aren't packaged for riscv64 on EPEL, so fall back to upstream's
+          # own devtools/emulate-tools.py, already used for the same gap on musllinux.
+          CIBW_BEFORE_ALL_LINUX: >-
+            dnf -y install zlib-devel bzip2-devel xz-devel &&
+            ( (dnf -y install epel-release && dnf -y install samtools bcftools htslib-tools) ||
+              for tool in samtools bcftools bgzip tabix; do
+                ln -sf {project}/devtools/emulate-tools.py /usr/local/bin/$tool
+              done )
+          CIBW_ENVIRONMENT: PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+
+      - name: Verify the wheel ships the compiled extensions and vendored licences
+        run: |
+          python3 - wheelhouse/*.whl <<'EOF'
+          import sys, zipfile
+          names = zipfile.ZipFile(sys.argv[1]).namelist()
+          sos = sorted(n for n in names if n.endswith(".so"))
+          print("\n".join(sos))
+          assert any("pysam/libc" in n for n in sos), sos
+
+          lic = sorted(n.split("/")[-1] for n in names if ".dist-info/licenses/" in n and not n.endswith("/"))
+          print("\n".join(lic))
+          assert {"COPYING", "LICENSE.htslib", "LICENSE.samtools", "LICENSE.bcftools"} <= set(lic), lic
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: pysam-${{ env.PYSAM_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish pysam ${{ inputs.version || '0.24.1' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: pysam-${{ inputs.version || '0.24.1' }}-*-manylinux_riscv64