cyvcf2: add build-cyvcf2.yml for riscv64 wheels

.github/workflows/build-cyvcf2.yml

@@ -0,0 +1,125 @@
+# SPDX-FileCopyrightText: 2026 The RISE Project
+# SPDX-License-Identifier: MIT
+---
+# This workflow is based on the `build_wheels` job of
+# https://github.com/brentp/cyvcf2/blob/v0.34.0/.github/workflows/wheels.yml
+name: Build cyvcf2 wheels (riscv64)
+
+on:
+  workflow_dispatch:
+    inputs:
+      version:
+        description: 'cyvcf2 version to build (git tag, e.g. 0.34.0)'
+        required: true
+        default: '0.34.0'
+  pull_request:
+    paths:
+      - '.github/workflows/build-cyvcf2.yml'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ inputs.version || '0.34.0' }}-${{ 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 0.34.0 there.
+  CYVCF2_VERSION: ${{ inputs.version || '0.34.0' }}
+  MANYLINUX_RISCV64_IMAGE: quay.io/pypa/manylinux_2_39_riscv64
+
+jobs:
+  setup:
+    uses: $/.github/workflows/_setup.yml
+
+  build_wheels:
+    needs: [setup]
+    name: Build cyvcf2 ${{ inputs.version || '0.34.0' }} ${{ matrix.python }}-manylinux_riscv64
+    runs-on: ubuntu-24.04-riscv
+    timeout-minutes: 90
+    strategy:
+      fail-fast: false
+      matrix:
+        python: ["cp312", "cp313", "cp314", "cp314t"]
+
+    steps:
+      - name: Checkout cyvcf2 v${{ env.CYVCF2_VERSION }}
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          repository: brentp/cyvcf2
+          ref: v${{ env.CYVCF2_VERSION }}
+          submodules: recursive
+          persist-credentials: false
+
+      - name: Checkout python-wheels
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1  # v7.0.1
+        with:
+          path: python-wheels
+          persist-credentials: false
+
+      - name: Patch cyvcf2 source
+        run: git apply python-wheels/patches/cyvcf2/${{ env.CYVCF2_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 }}
+          CIBW_BEFORE_ALL_LINUX: >-
+            dnf install -y autoconf automake libtool cmake ninja-build
+            zlib-devel bzip2-devel xz-devel
+          # No libcurl-devel and no EPEL on riscv64 (as build-pysam.yml/build-pybigwig.yml),
+          # so drop --enable-libcurl/--enable-s3/--with-libdeflate from upstream's own
+          # options; each defaults to "check" and htslib's configure silently disables it
+          # when the headers are absent instead of failing. bz2/lzma default to required,
+          # matching the devel packages installed above.
+          CIBW_ENVIRONMENT: >-
+            PIP_EXTRA_INDEX_URL=https://pypi.riseproject.dev/simple/
+            PIP_ONLY_BINARY=numpy
+            CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-lzma --enable-bz2"
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_SOURCES: cyvcf2/tests pyproject.toml
+          # test_reader.py/test_writer.py reach the compiled extension via a
+          # package-relative `from ..cyvcf2 import ...`, so cyvcf2/tests alone (no
+          # cyvcf2/__init__.py) isn't a deep enough package for that import to resolve.
+          # Merge the installed package (the compiled wheel) into the staged tree so the
+          # relative import lands on it directly, still exercising the compiled .so; its
+          # auditwheel-repaired RPATH is $ORIGIN-relative to a sibling cyvcf2.libs/
+          # (bz2/lzma), so stage that alongside it too.
+          CIBW_TEST_COMMAND: >-
+            site_pkg="$(python -c 'import cyvcf2, os; print(os.path.dirname(cyvcf2.__file__))')" &&
+            cp -a "$site_pkg/." cyvcf2/ &&
+            cp -a "$site_pkg/../cyvcf2.libs" . &&
+            python -m pytest -v cyvcf2/tests
+
+      - name: Verify the wheel ships the compiled extension 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("cyvcf2/cyvcf2" 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 {"LICENSE", "LICENSE.htslib", "LICENSE.htscodecs"} <= set(lic), lic
+          EOF
+
+      - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a  # v7.0.1
+        with:
+          name: cyvcf2-${{ env.CYVCF2_VERSION }}-${{ matrix.python }}-manylinux_riscv64
+          path: wheelhouse/*.whl
+          if-no-files-found: error
+
+  publish:
+    name: Publish cyvcf2 ${{ inputs.version || '0.34.0' }}
+    needs: [setup, build_wheels]
+    permissions:
+      contents: write
+      pull-requests: write
+    uses: $/.github/workflows/_publish-wheel.yml
+    with:
+      artifact-pattern: cyvcf2-${{ inputs.version || '0.34.0' }}-*-manylinux_riscv64

patches/cyvcf2/0.34.0/0001-Add-htslib-htscodecs-LICENSE-files-at-project-root.patch

@@ -0,0 +1,150 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Fri, 11 Sep 2026 13:07:54 +0200
+Subject: [PATCH] Add htslib/htscodecs LICENSE files at project root
+
+cyvcf2 statically links htslib (and its bundled htscodecs submodule) into
+the cyvcf2 extension by default on Linux (CYVCF2_HTSLIB_MODE=BUILTIN in
+CMakeLists.txt), but pyproject.toml sets no [project] license-files list.
+scikit-build-core's PEP 639 default license_files glob only covers
+LICEN[CS]E*/COPYING*/NOTICE*/AUTHORS* at the project root, so neither
+htslib's MIT/Expat-and-BSD LICENSE nor htscodecs' BSD LICENSE.md land in
+dist-info/licenses/ even though their code ships in every wheel.
+
+Copy each at the root as LICENSE.htslib and LICENSE.htscodecs, which the
+existing default glob already matches with no pyproject.toml change.
+
+Upstream-Status: To upstream [not submitted from this automated port run; needs a pull request against brentp/cyvcf2]
+---
+ LICENSE.htscodecs | 45 +++++++++++++++++++++++++++++++
+ LICENSE.htslib    | 69 +++++++++++++++++++++++++++++++++++++++++++++++
+ 2 files changed, 114 insertions(+)
+ create mode 100644 LICENSE.htscodecs
+ create mode 100644 LICENSE.htslib
+
+diff --git a/LICENSE.htscodecs b/LICENSE.htscodecs
+new file mode 100644
+index 0000000..14d3778
+--- /dev/null
++++ b/LICENSE.htscodecs
+@@ -0,0 +1,45 @@
++All files except those explicitly listed below are copyright Genome
++Research Limited and are made available under the BSD license.
++
++> Redistribution and use in source and binary forms, with or without
++> modification, are permitted provided that the following conditions
++> are met:
++> 
++>     (1) Redistributions of source code must retain the above copyright
++>     notice, this list of conditions and the following disclaimer. 
++> 
++>     (2) Redistributions in binary form must reproduce the above copyright
++>     notice, this list of conditions and the following disclaimer in
++>     the documentation and/or other materials provided with the distribution.  
++>     
++>     (3)The name of the author may not be used to endorse or promote
++>     products derived from this software without specific prior written
++>     permission.
++> 
++> THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
++> IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
++> WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
++> DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
++> INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
++> (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
++> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
++> HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
++> STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
++> IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
++> POSSIBILITY OF SUCH DAMAGE. 
++
++c_range_coder.h is Public Domain, derived from work by Eugene
++Shelwien.
++
++rANS_byte.h and rANS_word.h are derived from Fabien Giesen's work and
++is Public Domain.  https://github.com/rygorous/ryg_rans This work was
++in turn based on the ANS family of entropy encoders as described by
++Jarek Duda's paper: http://arxiv.org/abs/1311.2540
++
++> To the extent possible under law, Fabian Giesen has waived all
++> copyright and related or neighboring rights to ryg_rans, as
++> per the terms of the CC0 license:
++> 
++>   https://creativecommons.org/publicdomain/zero/1.0
++> 
++> This work is published from the United States.
+diff --git a/LICENSE.htslib b/LICENSE.htslib
+new file mode 100644
+index 0000000..925d47b
+--- /dev/null
++++ b/LICENSE.htslib
+@@ -0,0 +1,69 @@
++[Files in this distribution outwith the cram/ subdirectory are distributed
++according to the terms of the following MIT/Expat license.]
++
++The MIT/Expat License
++
++Copyright (C) 2012-2023 Genome Research Ltd.
++
++Permission is hereby granted, free of charge, to any person obtaining a copy
++of this software and associated documentation files (the "Software"), to deal
++in the Software without restriction, including without limitation the rights
++to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
++copies of the Software, and to permit persons to whom the Software is
++furnished to do so, subject to the following conditions:
++
++The above copyright notice and this permission notice shall be included in
++all copies or substantial portions of the Software.
++
++THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
++IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
++FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
++THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
++LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
++FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
++DEALINGS IN THE SOFTWARE.
++
++
++[Files within the cram/ subdirectory in this distribution are distributed
++according to the terms of the following Modified 3-Clause BSD license.]
++
++The Modified-BSD License
++
++Copyright (C) 2012-2023 Genome Research Ltd.
++
++Redistribution and use in source and binary forms, with or without
++modification, are permitted provided that the following conditions are met:
++
++1. Redistributions of source code must retain the above copyright notice,
++   this list of conditions and the following disclaimer.
++
++2. Redistributions in binary form must reproduce the above copyright notice,
++   this list of conditions and the following disclaimer in the documentation
++   and/or other materials provided with the distribution.
++
++3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute
++   nor the names of its contributors may be used to endorse or promote products
++   derived from this software without specific prior written permission.
++
++THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"
++AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
++IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
++DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE
++FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
++DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
++SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
++CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
++OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
++OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
++
++
++[The use of a range of years within a copyright notice in this distribution
++should be interpreted as being equivalent to a list of years including the
++first and last year specified and all consecutive years between them.
++
++For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
++2011-2012" should be interpreted as being identical to a notice that reads
++"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
++that reads "Copyright (C) 2005-2012" should be interpreted as being identical
++to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
++2011, 2012".]